pwem.protocols.protocol_import.images module

class pwem.protocols.protocol_import.images.ProtImportImages(**kwargs)

Bases: ProtImportFiles

Common protocol to import a set of images into the project.

fillAcquisition(acquisition)

Fill the acquition object with protocol params.

getAcquisition()

Build and fill an acquisition object.

getActions()

This method will allow that the ‘Stop import’ action to appears in the GUI when the user right-click in the protocol import box. It will allow a user to manually stop the streaming.

getFileNamesList()

Fill a list with the file names that contains extra folder

getFiles()

handleImgHed(copyOrLink, src, dst)

Check the special case of Imagic files format composed by two files: .hed and .img. When copying or linking we need to take care of the other one.

importImagesStep(pattern, voltage, sphericalAberration, amplitudeContrast, magnification)

Copy images matching the filename pattern Register other parameters.

importImagesStreamStep(pattern, voltage, sphericalAberration, amplitudeContrast, magnification)

Copy images matching the filename pattern Register other parameters.

iterNewInputFiles()

Iterate over input files that have not been imported. This function uses the self.importedFiles dict.

loadAcquisitionInfo()

Return a proper acquistionInfo (dict) or an error message (str).

processImportDict(importDict, importDir)

This function is used when we import a workflow from a json. If we need to include source data for reproducibility purposes, this function will make the necessary changes in the protocol dict to include the source data. Params:

• importDict: import dictionary coming from the json

• importDir: directory containing the json file

stopImport(e)

Since the actual protocol that is running is in a different process that the one that this method will be invoked from the GUI, we will use a simple mechanism to place an special file to stop the streaming.

stopStreamingFileExists()

classmethod validatePath(pathstr)